Those links are designed to work with pages that inherit from mojoBasePage, just using the same master page is not sufficient.
And the PageContent and PageSettings links will only appear on actual CMS pages not standalone pages.
I would look into which ajax extender you are using. While some of them use PageMethods whcih can only work in a page not a usercontrol, they usually also support using a web service, so you may be able to implement a web service and then use it in a usercontrol and call the web service instead of a page method.
Hope that helps,
Joe